Reference genome

Row

Table

Species Mean scaffold length (kbp) Number of scaffolds
Atherina boyeri 9.911369 100968
Coryphoblennius galerita 11.276056 64558
Coris julis 12.943508 62121
Dicentrarchus labrax 25997.621577 26
Diplodus puntazzo 9.583962 86517
Engraulis encrasicolus 2.760010 335460
Gobius niger 2.927332 216766
Hippocampus guttulatus 116.283677 3880
Lophius budegassa 76.885376 9523
Lithognathus mormyrus 9.167760 79966
Merluccius merluccius 7.105190 88639
Mullus surmuletus 19.830140 28381
Pagellus erythrinus 13.319614 58679
Serranus cabrilla 35.418556 18498
Spondyliosoma cantharus 30.373953 25731
Symphodus cinereus 12.448075 48250
Sardina pilchardus 8.098460 117259
Sarda sarda 30.836203 23941
Syngnathus typhle 39.258644 8628

Distribution

Packages used

       kableExtra       formattable               png            readxl            plotly             dplyr 
          "1.3.4"           "0.2.1"           "0.1-7"           "1.3.1"          "4.10.0"          "1.0.10" 
               DT           leaflet              ggsn           ggplot2 rnaturalearthdata     rnaturalearth 
           "0.20"           "2.1.1"           "0.5.0"           "3.4.0"           "0.1.0"           "0.1.0" 
               sf      RColorBrewer         rmarkdown     flexdashboard 
          "1.0-2"           "1.1-3"            "2.11"           "0.6.0" 
---
title: "Reference Genome"
author: "Pierre Barry"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
output: 
  flexdashboard::flex_dashboard:
    theme: paper
    orientation: rows
    social: menu
    source_code: embed
    vertical_layout: scroll
---

```{r global, include=FALSE}
list.of.packages <- c("RColorBrewer","formattable","kableExtra","ggplot2","plotly","png")

for (i in list.of.packages){
  if (i %in% installed.packages()[,"Package"] == FALSE){
    install.packages(i)
  }
  eval(bquote(library(.(i))))
}
```

```{r, include = FALSE}
color_med_atl=data.frame(Location=c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                         Col=brewer.pal(n = 4, name = "RdBu"))
```

Reference genome {data-icon="fa-keyboard-o"}
=======================================================================

```{r}
distri_length_reference_genome=vector('list',length(list.files(paste(path,"/data/reference_genome/",sep=""))))
for (i in 1:length(list.files(paste(path,"/data/reference_genome/",sep="")))){
  a<-read.table(paste(paste(path,"/data/reference_genome/",sep=""),list.files(paste(path,"/data/reference_genome/",sep=""))[i],sep=""))
  a<-a[,1]
  distri_length_reference_genome[[i]]=a
}
names(distri_length_reference_genome)=list.files(paste(path,"/data/reference_genome/",sep=""))
sp=list.files(paste(path,"/data/reference_genome/",sep=""))

length_distri=data.frame(Species=c(NA),
                         Num=c(NA),
                         length=c(NA))
for (i in 1:length(sp)){
  
  data_tmp=data.frame(Species=rep(sp[i],length(distri_length_reference_genome[[i]])),
                      Num=seq(1,length(distri_length_reference_genome[[i]])),
                      length=distri_length_reference_genome[[i]])
  
  length_distri=rbind(length_distri,
                      data_tmp)
  
}

length_distri=length_distri[-1,]

mean_length=c()
number_scaff=c()
for (i in 1:length(levels(factor(length_distri$Species)))){
  mean_length[i]=mean(length_distri$length[length_distri$Species==levels(factor(length_distri$Species))[i]])
  number_scaff[i]=length(length_distri$length[length_distri$Species==levels(factor(length_distri$Species))[i]])
}
names(mean_length)=levels(factor(length_distri$Species))
names(number_scaff)=levels(factor(length_distri$Species))

DATA_REFERENCE_GENOME=data.frame(Species=names(mean_length),
                                 Mean_length=as.vector(mean_length)/1000,
                                 Number_scaffold=as.vector(number_scaff))

ref_table=data.frame(NAME=c("0-1e+4",
                            "1e+4-1e+5",
                            "1e+5-1e+6",
                            "1e+6-1e+7",
                            "1e+7-1e+8"),
                     MIN=c(0,1e+4,1e+5,1e+6,1e+7),
                     MAX=c(1e+4,1e+5,1e+6,1e+7,1e+8))


tmp=ifelse(length_distri$length < 1e+4, "0-1e+4", length_distri$length)
tmp=ifelse(length_distri$length >= 1e+4 & length_distri$length<1e+5, "1e+4-1e+5", tmp)
tmp=ifelse(length_distri$length >= 1e+5 & length_distri$length<1e+6, "1e+5-1e+6", tmp)
tmp=ifelse(length_distri$length >= 1e+6 & length_distri$length<1e+7, "1e+6-1e+7", tmp)
tmp=ifelse(length_distri$length >= 1e+7 & length_distri$length<1e+8, "1e+7-1e+8", tmp)

length_distri$group=tmp


DATA_REFERENCE_GENOME$Mean_length <- color_bar("lightgreen")(DATA_REFERENCE_GENOME$Mean_length)
DATA_REFERENCE_GENOME$Number_scaffold <- color_bar("lightgreen")(DATA_REFERENCE_GENOME$Number_scaffold)

DATA_REFERENCE_GENOME$Species = c("Atherina boyeri",
                             "Coryphoblennius galerita",
                             "Coris julis",
                             "Dicentrarchus labrax",
                             "Diplodus puntazzo",
                             "Engraulis encrasicolus",
                             "Gobius niger",
                             "Hippocampus guttulatus",
                             "Lophius budegassa",
                             "Lithognathus mormyrus",
                             "Merluccius merluccius",
                             "Mullus surmuletus",
                             "Pagellus erythrinus",
                             "Serranus cabrilla",
                             "Spondyliosoma cantharus",
                             "Symphodus cinereus",
                             "Sardina pilchardus",
                             "Sarda sarda",
                             "Syngnathus typhle")
```

Row {.tabset}
-----------------------------------------------------------------------

### Table

```{r, fig.height=75}
DATA_REFERENCE_GENOME$Species = cell_spec(DATA_REFERENCE_GENOME$Species,italic = T)

kbl(DATA_REFERENCE_GENOME,col.names = c("Species",
                           "Mean scaffold length (kbp)",
                           "Number of scaffolds")
    ,escape = F,align=c(rep('c',times=2))) %>%
  kable_classic ("striped","hover",full_width = T,html_font = "Cambria")  %>%
  kable_paper("hover", full_width = F) %>%
  column_spec(1, width = "10cm") %>%
  column_spec(2, width = "10cm") %>%
  column_spec(3, width = "7.5cm")
```

### Distribution 

```{r, fig.height=75}
p<-ggplot(length_distri,aes(x=length,fill=group))+
  geom_histogram(alpha=0.5,col="darkblue",bins=200)+
  scale_color_viridis_d()+
  theme_classic()+
  xlab("Length")+
  ylab("Frequency")+
  scale_x_log10()+
  scale_y_log10()+
  facet_grid(Species ~ .)+
  theme(strip.background = element_rect(fill="white"),
        strip.text.y = element_text(size=12, color="darkblue",
                                    face="bold"))+
  scale_fill_viridis_d()

ppp<-ggplotly(p,height=5000)  %>% partial_bundle() %>% hide_legend()

img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
vv[19]=0.75
yy<-seq(0.98,0.03,length.out=19)
size.x=0.075
ppp<-  ppp %>%
  layout(
    images = list(
      list(
        source = raster2uri(as.raster(img1)),
        x = vv[19], y = yy[1], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img3)),
        x = vv[19], y = yy[2], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img4)),
        x = vv[19], y = yy[3], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img5)),
        x = vv[19], y = yy[4], 
        sizex = size.x, sizey = 0.05
      ),
      list(
        source = raster2uri(as.raster(img6)),
        x = vv[19], y = yy[5], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img7)),
        x = vv[19], y = yy[6], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img8)),
        x = vv[19], y = yy[7], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img9)),
        x = vv[19], y = yy[8], 
        sizex = size.x, sizey = 0.025
      ),
      list(
        source = raster2uri(as.raster(img10)),
        x = vv[19], y = yy[9], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img11)),
        x = vv[19], y = yy[10], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img12)),
        x = vv[19], y = yy[11], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img13)),
        x = vv[19], y = yy[12], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img14)),
        x = vv[19],y = yy[13], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img15)),
        x = vv[19], y = yy[14], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img16)),
        x = vv[19], y = yy[15], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img17)),
        x = vv[19], y = yy[16], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img18)),
        x = vv[19], y = yy[17], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img19)),
        x = vv[19], y = yy[18], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img20)),
        x = vv[19], y = yy[19], 
        sizex = size.x, sizey = 0.1
      )
    )
  ) 
ppp
```

Packages used {data-icon="fa-map"}
=======================================================================

```{r}
installed.packages()[names(sessionInfo()$otherPkgs), "Version"]
```